GEO series

An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms

GSE306294 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2026/01/30 Platform GPL34284

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanismsbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

RNA polymerase III (Pol III) produces a plethora of small noncoding RNA species involved in diverse cellular processes, from transcription regulation and splicing to RNA stability, translation, and proteostasis. Though Pol III activity is broadly coupled with cellular demands for protein synthesis and growth, a more precise understanding of gene-level dynamics and context-specific expression patterns remains missing, in part due to multiple challenges related to sequencing and mapping Pol III-derived small ncRNAs.

Read the full summary ↓

Here, we establish a predictive multi-tissue map of Pol III activity across 19 tissues and 22 primary cancers by comprehensively profiling the chromatin accessibility of canonical Pol III-transcribed gene classes. Our framework relies on the unique relationship between gene accessibility and Pol III transcription, inferring activity through uniform binary classification of ATAC-seq enrichment at Pol III-transcribed genes. By characterizing multi-context gene uniformity, we provide a definition of the core Pol III transcriptome, broadly active across specialized tissues, and catalog genes with varied levels of context specificity. Our genomic Pol III atlas uncovers variable levels of activity across tissues, including sharp contraction of the Pol III transcriptome in heart and brain tissues and frequent expansion across diverse cancers. We show that both tissue- and tumor-specific genes are significantly enriched within lamina-associated domains (LADs), and that aberrant expression of nuclear lamin proteins is sufficient to induce Pol III- emergent patterns at tumor-specific genes. Together, these findings link Pol III dynamics to subnuclear compartment- alization and provide a resource for better understanding Pol III expansion and small RNA biogenesis in cancer.

Published in

An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms

Lizarazo S, Zhou S, Cheng R et al. · bioRxiv : the preprint server for biology 2025 · PMID 40949979 · doi:10.1101/2025.08.28.672650

This dataset

Open GSE306294 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE306294_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1310424 and SRA study SRP612244. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40949979) ↗

Study design

24 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 24 sample titles: 24 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM9196903 HEK293 , GFP , Rep1 , smallRNA
GSM9196904 HEK293 , GFP , Rep2 , smallRNA
GSM9196905 HEK293 , GFP , Rep3 , smallRNA
GSM9196906 HEK293 , LMNA , Rep1 , smallRNA
GSM9196907 HEK293 , LMNA , Rep2 , smallRNA
GSM9196908 HEK293 , LMNA , Rep3 , smallRNA
GSM9196909 HEK293 , LMNB1 , Rep1 , smallRNA
GSM9196910 HEK293 , LMNB1 , Rep2 , smallRNA
GSM9196911 HEK293 , LMNB1 , Rep3 , smallRNA
GSM9196912 HEK293 , LMNB2 , Rep1 , smallRNA
GSM9196913 HEK293 , LMNB2 , Rep2 , smallRNA
GSM9196914 HEK293 , LMNB2 , Rep3 , smallRNA
GSM9196915 HEK293 , GFP , Rep1 , ATAC
GSM9196916 HEK293 , GFP , Rep2 , ATAC
GSM9196917 HEK293 , GFP , Rep3 , ATAC
GSM9196918 HEK293 , LMNA , Rep1 , ATAC
GSM9196919 HEK293 , LMNA , Rep2 , ATAC
GSM9196920 HEK293 , LMNA , Rep3 , ATAC
GSM9196921 HEK293 , LMNB1 , Rep1 , ATAC
GSM9196922 HEK293 , LMNB1 , Rep2 , ATAC
GSM9196923 HEK293 , LMNB1 , Rep3 , ATAC
GSM9196924 HEK293 , LMNB2 , Rep1 , ATAC
GSM9196925 HEK293 , LMNB2 , Rep2 , ATAC
GSM9196926 HEK293 , LMNB2 , Rep3 , ATAC

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GSE311392 The NuRD chromatin remodeling complex regulates tRNA genes through direct interactions with RNA polymerase III [Nuclei run-on (nascent RNA) profiling] 6 samples shares iii, polymerase

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.